She left the story editor position before the third season went into production: "I had told Gene Roddenberry that I did not wish to continue on Star Trek as story editor because I wanted to freelance and write for other series. I did, however, want to continue to do scripts for Star Trek. Gene was agreeable to this, and I was given a contract in February of 1968 which called for a guarantee of three scripts, with an option for three more. Whenever anyone has asked why I chose to leave Star Trek's story editorship, I have always given this reply." [1]

In the DS9 episode "Far Beyond the Stars", the character Kay Eaton, who had to pose as a male to get her science fiction stories published, was an homage to Fontana.

In 2006, she gave an interview to Star Trek Monthly in which she talked about writing for three Star Trek series. She notes how unhappy she was with the way Gene Roddenberry re-wrote the episodes they wrote together. She used the pseudonym "J. Michael Bingham" for "The Naked Now", as she was especially unhappy with the episode. She liked writing "Dax" much more.

Outside of Trek, Fontana wrote scripts for dozens of shows, including Babylon 5 and Earth: Final Conflict. In a 1974 episode scripted for The Six Million Dollar Man, "The Rescue of Athena One", Fontana pays homage to Star Trek by having Lee Majors' character of Colonel Steve Austin speak the line "Space... it really is the final frontier, isn't it?"

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